Journal: BMC Microbiology

Article Title: Metaproteomics reveals insights into microbial structure, interactions, and dynamic regulation in defined communities as they respond to environmental disturbance

doi: 10.1186/s12866-021-02370-4

Figure Lengend Snippet: Assessment of microbial population size. ( A ) Microbial community composition from cell pellets using metaproteomics was estimated by total protein count for each community passaged in defined media MOPS + glucose (MOPS) or complex (R2A) media. There was a total of 15 passages per medium and 3 biological replicates per passage. Individual colors in the stacked bar charts represent each microbial member. ( B ) Cellular estimates of organism relative abundance plotted against extracellular estimates of organism abundance for each passage for MOPS (black circles) and R2A (red circles). Each circle represents the averaged abundance across replicates for a single passage. Proteome depth (number of proteins identified) is plotted for each microbe per sample measured in the defined microbial community passaged across (C) defined MOPS + glucose (black) and (D) complex R2A (red) media

Article Snippet: Equal volumes of all 10 isolates with the same normalized OD 600 were mixed in 10 mL of R2A complex medium (Teknova, # R0005) [ ] and 10 mL of MOPS minimal medium [ ] supplemented with 0.2 % glucose at 30 °C with shaking at 200 rpm.

Techniques: Metaproteomics

Journal: BMC Microbiology

Article Title: Metaproteomics reveals insights into microbial structure, interactions, and dynamic regulation in defined communities as they respond to environmental disturbance

doi: 10.1186/s12866-021-02370-4

Figure Lengend Snippet: Metaproteomics analysis of Pseudomonas sp. GM17 functional behavior during community assembly. ( A ) Overlap of proteins identified between both media. Each node represents a unique protein accession, and the color indicates whether the relative protein abundance changed significantly based on ANOVA in one (yellow) or both media (red) or not significant in either (grey). Figure generated using DiVenn 2.0. ( B ) Relative protein abundance for the GacS sensor histidine kinase and the GacA response regulator in MOPS (black) or R2A media (red). Error bars represent standard error for each set of biological triplicates. ( C ) Heatmap (one-way clustering using ward method) illustration for 18 antibiotic and secondary metabolite gene clusters predicted by antiSMASH v5.0. Color gradient represents the percentage of proteins identified for a given gene cluster. ( D ). Heatmap (one-way clustering using ward method) illustration of relative protein abundances for proteins encoded by the 18 antibiotic and secondary metabolite gene clusters. Color gradient represents a standardized score calculated per protein and white represents proteins that were not quantified in a particular medium

Article Snippet: Equal volumes of all 10 isolates with the same normalized OD 600 were mixed in 10 mL of R2A complex medium (Teknova, # R0005) [ ] and 10 mL of MOPS minimal medium [ ] supplemented with 0.2 % glucose at 30 °C with shaking at 200 rpm.

Techniques: Metaproteomics, Functional Assay, Generated

Journal: BMC Microbiology

Article Title: Metaproteomics reveals insights into microbial structure, interactions, and dynamic regulation in defined communities as they respond to environmental disturbance

doi: 10.1186/s12866-021-02370-4

Figure Lengend Snippet: Metaproteomics analysis of Pantoea sp. YR343 functional behavior during community assembly. ( A ) Relative abundance of Pantoea organism abundance in MOPS and R2A media based on metaproteomics data. ( B ) Relative abundance across R2A passages for geranylgeranyl pyrophosphate synthase and phytoene desaturase, two key proteins involve in carotenoid biosynthesis. Error bars represent standard error for each set of biological triplicates. The dashed arrow in the flow diagram represents multiple steps in biosynthesis. ( C ) Heatmap of relative protein abundance for proteins involved in aerobic/anaerobic respiration and motility. ( D ) Relative abundances for proteins associated with defense responses to antagonist behaviors. Error bars represent standard error for each set of biological triplicates

Article Snippet: Equal volumes of all 10 isolates with the same normalized OD 600 were mixed in 10 mL of R2A complex medium (Teknova, # R0005) [ ] and 10 mL of MOPS minimal medium [ ] supplemented with 0.2 % glucose at 30 °C with shaking at 200 rpm.

Techniques: Metaproteomics, Functional Assay

Journal: BMC Microbiology

Article Title: Metaproteomics reveals insights into microbial structure, interactions, and dynamic regulation in defined communities as they respond to environmental disturbance

doi: 10.1186/s12866-021-02370-4

Figure Lengend Snippet: Dynamic regulation of methylation modification in lysine (K) residue of EF-Tu in nutrient-deprived organisms. Percentage abundances of K-methylated modified and unmodified peptides in the Elongation factor Tu proteins of ( A ) Pantoea sp. YR343 and ( B ) Rhizobium sp. CF142 in R2A media. ( C ) Multiple sequence alignment was performed for all Elongation Factor Tu proteins identified by metaproteomics in this study. The lysine amino acid position where the modification occurs in this study is highlighted with a red arrow. Unlike other organisms, Bacillus sp. BC15 and Sphingobium sp. AP49 have an arginine (R) residue at this position and no methylation modifications were observed for these protein sequences. For reference, the Elongation factor TU sequence of E. coli (strain K12) was added for comparison

Article Snippet: Equal volumes of all 10 isolates with the same normalized OD 600 were mixed in 10 mL of R2A complex medium (Teknova, # R0005) [ ] and 10 mL of MOPS minimal medium [ ] supplemented with 0.2 % glucose at 30 °C with shaking at 200 rpm.

Techniques: Methylation, Modification, Residue, Sequencing, Metaproteomics, Comparison

Journal: Microbiology Resource Announcements

Article Title: Complete Genome Sequence of Rhodococcus ruber R1, a Novel Strain Showing a Broad Catabolic Potential toward Lignin-Derived Aromatics

doi: 10.1128/MRA.00905-19

Figure Lengend Snippet: Growth of Rhodococcus ruber R1 on several lignocellulose-related aromatic compounds. The growth of strain R1 on 2 mM guaiacol (A), p -cresol (B), p -coumarate (C), phenol (D), m -cresol (E), and 4-hydroxybenzoate (F) as the sole carbon and energy sources was assessed. All reagents were of analytical grade and were obtained from Sigma-Aldrich (Buchs, Switzerland). The cultures were incubated in a 96-well microplate (Thermo Fisher Scientific, Rochester, NY, USA), with agitation, for 15 min at 30°C, and the optical density at 600 nm (OD 600 ) was measured with a Synergy HTX multimode reader (BioTek, Winooski, VT, USA). Minimal salt medium without carbon sources (control) supported minor growth, which was subtracted from the growth curves for medium with carbon sources. Cell cultures were inoculated with 100-fold dilutions of overnight cultures of strain R1 grown on R2A broth. Five replicates were performed for growth measurements. Error bars represent 1 standard deviation.

Article Snippet: Genomic DNA of R. ruber R1 cells cultivated in R2A broth (Neogen) was obtained using the GenElute kit (Sigma-Aldrich), and sequencing was accomplished by combining Illumina and PacBio technology.

Techniques: Incubation, Standard Deviation

Journal: Microorganisms

Article Title: Excessive Extracellular Ammonium Production by a Free-Living Nitrogen-Fixing Soil Clostridium sp. Strain

doi: 10.3390/microorganisms12122634

Figure Lengend Snippet: Changes of extracellular NH 4 + concentration and biomass (OD 600 ) during the anaerobic cultivation of three Clostridium strains, such as OS1-26, KCTC 1674 T , and KCTC 1790 T , by incubation time in R2A medium.

Article Snippet: Various temperature (10, 25, 30, 35, and 40 °C), pH (4, 5, 6, 7, 8, 9, and 10), and NaCl (0, 0.5, 1, 1.5, and 2%) conditions were tested for growth in R2A broth contained in Hungate anaerobic culture tubes (Chemglass, Vineland, NJ, USA) flushed and filled with N 2 during 6 days of incubation at 200 rpm in an orbital shaker.

Techniques: Concentration Assay, Incubation

Journal: Microorganisms

Article Title: Excessive Extracellular Ammonium Production by a Free-Living Nitrogen-Fixing Soil Clostridium sp. Strain

doi: 10.3390/microorganisms12122634

Figure Lengend Snippet: Transcription levels of nifH gene of Clostridium sp. OS1-26 during the anaerobic cultivation in R2A medium. Transcription levels were normalized by the number of 16S rRNA copies. Statistical significance was determined by one-way ANOVA followed by Tukey’s post hoc test. p > 0.05 (ns), p < 0.01 (**), p < 0.001 (***).

Article Snippet: Various temperature (10, 25, 30, 35, and 40 °C), pH (4, 5, 6, 7, 8, 9, and 10), and NaCl (0, 0.5, 1, 1.5, and 2%) conditions were tested for growth in R2A broth contained in Hungate anaerobic culture tubes (Chemglass, Vineland, NJ, USA) flushed and filled with N 2 during 6 days of incubation at 200 rpm in an orbital shaker.

Techniques: